Meshes going berserk when extruding
Ah, I found the issue. 



I have two entrances to the house, a front door and a back door. To prepare for the extrude for the foundation, I added a edge below the doors, so it would make a face when extruded.

It seems that extruding non-faces is causing issues in Blender, and that's what was causing my issues. 

Removing these edges before extruding works. So I can simply fill the faces after extruding.